NEW SPECIES
‘Bittarella massiliensis’ gen. nov., sp. nov. isolated by culturomics from the gut of a healthy 28-year-old man
G. A. Durand1, P.-E. Fournier1, D. Raoult1,2and S. Edouard1
1)Aix-Marseille Université, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE), UM63, CNRS 7278, IRD 198, INSERM U1095, Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France and2)Special Infectious Agents Unit, King Fahd Medical Research Centre, King Abdulaziz University, Jeddah, Saudi Arabia
Abstract
We report here the main features of the proposed new bacterial genusBittarella.The type strain‘Bittarella massiliensis’GD6T(CSUR P2149) was isolated from a stool sample from a healthy French man.
© 2017 The Authors. Published by Elsevier Ltd on behalf of European Society of Clinical Microbiology and Infectious Diseases.
Keywords:Anaerobe,‘Bittarella massiliensis’gen. nov., sp. nov., culturomics, gut microbiota, taxono-genomics
Original Submission:30 November 2016;Revised Submission:14 December 2016;Accepted:14 December 2016 Article published online:19 December 2016
Corresponding author:S. Edouard, URMITE UM63, CNRS7278, IRD198, INSERM1095, Faculté de Médecine, Aix Marseille Université, 27 boulevard Jean Moulin, 13385 Marseille cedex 5, France E-mail:[email protected]
We isolated in April 2015, as part of the culturomics study of the Human Microbiome [1], an oxygen-intolerant species that could not be identified by matrix-assisted laser desorption/
ionization time-of-flight mass spectrometry (MALDI-TOF MS) screening (score <1.7) using a Microflex spectrometer (Bruker Daltonics, Bremen, Germany)[1–3]. The species was isolated from the faeces of a healthy, 28-year-old French man. The stool was inoculated without delay in different culture conditions used for culturomics[1]. The initial growth of the GD6 strain occurred after 48 h of anaerobic incubation in a 5% sheep blood-enriched Columbia agar (bioMérieux, Marcy l’Etoile, France). The stool was pre-incubated for 10 days at 37°C in an anaerobic atmosphere in a culture bottle in the presence of 5%
sheep blood and 5% rumenfluidfilter-sterilized through a 0.2- μm-pore filter (Thermo Fisher Scientific, Villebon sur Yvette, France). The donor gave signed informed consent and the study was validated by the ethics committee of the Institut Fédératif de Recherche IFR48 under number 09-022.
The colonies appeared to be 0.5 mm in size, homogeneous, translucent, smooth and non-haemolytic. Strain GD6 was a non-
motile, Gram-negative and rod-shaped bacteria with a mean diameter of 250 nm and a length of 1μm without spore-forming activity. Catalase and oxidase were negative. The complete 16S rRNA gene of the bacterium was sequenced as previously described[4]and shared 89.5% of identity with Anaerotruncus massiliensisstrain AT3 (GenBank Accession number LN866995) [5]. The phylogenetically closest species standing in nomencla- ture wasHydrogenoanaerobacterium saccharovoranswith 89.2% of similarity (Fig. 1). The phylogenetic analysis confirms the bac- terium as a member within theRuminococcaceaefamily belonging to the phylumFirmicutes(Fig. 1).Hydrogenoanaerobacterium sac- charovorans is an anaerobic, hydrogenogenic, rod-shaped bac- terium isolated from a laboratory-scale H2-producing up-flow anaerobic sludge blanket reactor[6].
Strain GD6 exhibits a 16S rRNA sequence divergence >5%
with its phylogenetically closest species with a validly published name standing in nomenclature[7], so we propose the creation of the genus‘Bittarella’whose type strain is‘Bittarella massiliensis’ GD6T (Bit.ar. Masc. Adj., in honour of Dr Bittar, a French microbiologist, and mas.il.i.en’sis. L. gen. masc. n.massiliensis, of Massilia, the Latin name of Marseille where the strain GD6Twas first isolated).
MALDI-TOF-MS spectrum accession number. The MALDI-TOF-MS spectrum of‘Bittarella massiliensis’is available at http://mediterranee-infection.com/article.php? laref=256&
titre=urms-database. (Last accessed 28 November 2016).
New Microbe and New Infect2017;16:28–29
© 2017 The Authors. Published by Elsevier Ltd on behalf of European Society of Clinical Microbiology and Infectious Diseases This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/) http://dx.doi.org/10.1016/j.nmni.2016.12.014
Nucleotide sequence accession number. The 16S rRNA gene sequence was deposited in GenBank under Accession number LN881596.
Deposit in a culture collection. Strain GD6T was deposited in the collection de Souches de l’Unités des Rick- ettsies (CSUR, WDCM 875) under number P2149.
Transparency declaration
No conflicts of interest are declared.
Acknowledgements
This work was funded by the Mediterrannée-Infection Foun- dation. We thank Magdalen Lardière for English revision.
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FIG. 1.Phylogenetic tree based on the 16S rRNA gene sequence showing the position ofBittarella massiliensisGD6T(bold) with other closely related species among theRuminococcaceae. The EMBL database accession numbers are indicated in parentheses. Sequences were aligned usingCLUSTALW, and phylogenetic inferences were obtained with a Kimura two-parameter model using the neighbour-joining method with 1000 bootstrap replicates, within MEGA6 software. The scale bar represents a 2% nucleotide sequence divergence.
NMNI Durandet al. ‘Bittarella massiliensis’gen. nov., sp. nov. 29
© 2017 The Authors. Published by Elsevier Ltd on behalf of European Society of Clinical Microbiology and Infectious Diseases,NMNI,16, 28–29 This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).